Report for BC01

Quality Control

  1. Porechop was run to trim adapter sequences from reads and discard reads with adapters found in the middle. More detailed information can be found in porechop_log. For quality control plots of the reads after this step, see plot_pre_filter.
  2. Reads were aligned to the TB reference NC_000962.3.fa using Minimap2.
  3. All reads which did not map to NC_000962.3.fa were removed. Prior to filtering there were 143590 reads. After filtering there remains 142031. This means 98.91% of reads mapped to NC_000962.3.fa. For more stats on the pre-filtered reads see stats_pre_filter and for post-filtered reads see stats_post_filter. For quality control plots of the reads after this step (and read percent identity to NC_000962.3.fa) see plot_post_filter. Stats were produced with NanoStat and plots with Pistis.

Mykrobe Analysis

Phylogenetic group: Mycobacterium_tuberculosis_complex

Species: Mycobacterium_tuberculosis

Lineage: Beijing_East_Asia

A summary of the susceptiblity information from Mykrobe predict is shown here. For the full report, see mykrobe. If resistance is identified for a drug then the predicted responsible variant(s) is given, along with supporting information.

plot_post_filter:
BC01_post_filtering.pdf
plot_pre_filter:
BC01_pre_filtering.pdf
porechop_log:
porechop.log
stats_post_filter:
BC01_post_filtering.txt
stats_pre_filter:
BC01_pre_filtering.txt
Author: Michael Hall (michael.hall@ebi.ac.uk) | 2018-06-20